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Sebé-Pedrós, Arnau, Tanay, Amos, Lawniczak, Mara KN, Arendt, Detlev, Aerts, Stein, Archibald, John, Arnone, Maria Ina, Blaxter, Mark, Cleves, Phillip, Coelho, Susana M, Dias, Mafalda, Dunn, Casey, Elek, Anamaria, Frazer, Jonathan, Gabaldón, Toni, Gillis, Jesse, Grau-Bové, Xavier, Guigó, Roderic, Hobert, Oliver, Huerta-Cepas, Jaime, Irimia, Manuel, Klein, Allon, Lewin, Harris, Lowe, Christopher J, Marlow, Heather, Musser, Jacob M, Nagy, László G, Najle, Sebastián R, Pachter, Lior, Paez, Sadye, Papatheodorou, Irene, Passalacqua, Michael J, Rajewsky, Nikolaus, Rhee, Seung Y, Richards, Thomas A, Sauka-Spengler, Tatjana, Saunders, Lauren M, Seuntjens, Eve, Solana, Jordi, Song, Yuyao, Technau, Ulrich, Wang, Bo, Biodiversity Cell Atlas meeting participants (September 2025) The Biodiversity Cell Atlas: mapping the tree of life at cellular resolution. Nature, 645 (8082). pp. 877-885. ISSN 0028-0836

Xu, Xiaosa, Passalacqua, Michael, Rice, Brian, Demesa-Arevalo, Edgar, Kojima, Mikiko, Takebayashi, Yumiko, Yu, Xingyao, Harris, Benjamin, Liu, Yuchen, Gallavotti, Andrea, Sakakibara, Hitoshi, Gillis, Jesse, Jackson, David (August 2025) Large-scale single-cell profiling of stem cells identifies redundant regulators of shoot development and yield trait variation. Developmental Cell. S1534-5807(25)00500. ISSN 1534-5807

Benoit, Matthias, Jenike, Katharine M, Satterlee, James W, Ramakrishnan, Srividya, Gentile, Iacopo, Hendelman, Anat, Passalacqua, Michael J, Suresh, Hamsini, Shohat, Hagai, Robitaille, Gina M, Fitzgerald, Blaine, Alonge, Michael, Wang, Xingang, Santos, Ryan, He, Jia, Ou, Shujun, Golan, Hezi, Green, Yumi, Swartwood, Kerry, Karavolias, Nicholas G, Sierra, Gina P, Orejuela, Andres, Roda, Federico, Goodwin, Sara, McCombie, W Richard, Kizito, Elizabeth B, Gagnon, Edeline, Knapp, Sandra, Särkinen, Tiina E, Frary, Amy, Gillis, Jesse, Van Eck, Joyce, Schatz, Michael C, Lippman, Zachary B (March 2025) Solanum pan-genetics reveals paralogues as contingencies in crop engineering. Nature. ISSN 0028-0836 (Public Dataset)

Benoit, Matthias, Jenike, Katharine M, Satterlee, James W, Ramakrishnan, Srividya, Gentile, Iacopo, Hendelman, Anat, Passalacqua, Michael J, Suresh, Hamsini, Shohat, Hagai, Robitaille, Gina M, Fitzgerald, Blaine, Alonge, Michael M, Wang, Xingang, Santos, Ryan, He, Jia, Ou, Shujun, Golan, Hezi, Green, Yumi, Swartwood, Kerry, Sierra, Gina P, Orejuela, Andres, Fornaguera, Federico, Goodwin, Sara, McCombie, William Richard, Kizito, Elizabeth Balyejusa, Gagnon, Edeline, Knapp, Sandra, Sarkinen, Tiina, Frary, Amy, Gillis, Jesse, Van Eck, Joyce, Schatz, Michael C, Lippman, Zachary B (September 2024) Solanum pan-genomics and pan-genetics reveal paralogs as contingencies in crop engineering. bioRxiv. ISSN 2692-8205 (Submitted)

Satterlee, James W, Alonso, David, Gramazio, Pietro, Jenike, Katharine M, He, Jia, Arrones, Andrea, Villanueva, Gloria, Plazas, Mariola, Ramakrishnan, Srividya, Benoit, Matthias, Gentile, Iacopo, Hendelman, Anat, Shohat, Hagai, Fitzgerald, Blaine, Robitaille, Gina M, Green, Yumi, Swartwood, Kerry, Passalacqua, Michael J, Gagnon, Edeline, Hilgenhof, Rebecca, Huggins, Trevis D, Eizenga, Georgia C, Gur, Amit, Rutten, Twan, Stein, Nils, Yao, Shengrui, Poncet, Adrien, Bellot, Clement, Frary, Amy, Knapp, Sandra, Bendahmane, Mohammed, Särkinen, Tiina, Gillis, Jesse, Van Eck, Joyce, Schatz, Michael C, Eshed, Yuval, Prohens, Jaime, Vilanova, Santiago, Lippman, Zachary B (August 2024) Convergent evolution of plant prickles by repeated gene co-option over deep time. Science, 385 (6708). eado1663. ISSN 0036-8075 (Public Dataset)

Passalacqua, Michael John, Gillis, Jesse (June 2024) Coexpression enhances cross-species integration of single-cell RNA sequencing across diverse plant species. Nature Plants. ISSN 2055-0278 (Public Dataset)

Satterlee, James W, Alonso, David, Gramazio, Pietro, Jenike, Katharine M, He, Jia, Arrones, Andrea, Villanueva, Gloria, Plazas, Mariola, Ramakrishnan, Srividya, Benoit, Matthias, Gentile, Iacopo, Hendelman, Anat, Shohat, Hagai, Fitzgerald, Blaine, Robitaille, Gina M, Green, Yumi, Swartwood, Kerry, Passalacqua, Michael J, Gagnon, Edeline, Hilgenhof, Rebecca, Huggins, Trevis D, Eizenga, Georgia C, Gur, Amit, Rutten, Twan, Stein, Nils, Yao, Shengrui, Bellot, Clement, Bendahmane, Mohammed, Frary, Amy, Knapp, Sandra, Särkinen, Tiina, Gillis, Jesse, Van Eck, Joyce, Schatz, Michael C, Eshed, Yuval, Prohens, Jaime, Vilanova, Santiago, Lippman, Zachary B (February 2024) Convergent evolution of plant prickles is driven by repeated gene co-option over deep time. bioRxiv. (Submitted)

Passalacqua, Michael John, Gillis, Jesse (November 2023) Coexpression enhances cross-species integration of scRNA-seq across diverse plant species. bioRxiv. (Submitted)

Guillotin, Bruno, Rahni, Ramin, Passalacqua, Michael, Mohammed, Mohammed Ateequr, Xu, Xiaosa, Raju, Sunil Kenchanmane, Ramírez, Carlos Ortiz, Jackson, David, Groen, Simon C, Gillis, Jesse, Birnbaum, Kenneth D (May 2023) A pan-grass transcriptome reveals patterns of cellular divergence in crops. Nature, 617 (7962). pp. 785-791. ISSN 0028-0836